Cooperativity in hydrogen-bonded interactions: ab initio and "atoms in molecules" analyses

The H(2)CO...(HF)(n) (n = 1, ..., 9) complexes were investigated using the MP2 method and the following basis sets: 6-311++G(d,p), aug-cc-pVDZ and aug-cc-pVTZ. It was found that the cooperativity effect enhances significantly the F-H...O hydrogen bond; in some of cases one can detect the covalent nature of hydrogen bonding. To deepen the nature of the interactions investigated, the scheme of decomposition of the interaction energy was applied; for stronger H-bonds where the cooperativity is more important, the delocalization energy term increases. The ratio of delocalization energy to electrostatic energy increases for stronger hydrogen bonds where the proton...acceptor distance is shorter. The Bader theory was also applied, and it was found that for stronger H-bonds the electronic energy density at the proton...acceptor bond critical point is negative and may be attributed to the partly covalent interaction.     

Insertion of rare gas atoms into BF3 and AlF3 molecules: an ab initio investigation

The structure, stability, charge redistribution, and harmonic vibrational frequencies of rare gas inserted group III-B fluorides with the general formula F-Rg-MF(2) (where M=B and Al; Rg=Ar, Kr, and Xe) have been investigated using ab initio quantum chemical methods. The Rg atom is inserted in one of the M-F bond of MF(3) molecules, and the geometries are optimized for ground as well as transition states using the MP2 method. It has been found that Rg inserted F-Rg-M portion is linear in both F-Rg-BF(2) and F-Rg-AlF(2) species. The binding energies corresponding to the lowest energy fragmentation products MF(3)+Rg (two-body dissociation) have been computed to be -670.4, -598.8, -530.7, -617.0, -562.1, and -494.0 kJmol for F-Ar-BF(2), F-Kr-BF(2), F-Xe-BF(2), F-Ar-AlF(2), F-Kr-AlF(2), and F-Xe-AlF(2) species, respectively. The dissociation energies corresponding to MF(2)+Rg+F fragments (three-body dissociation) are found to be positive with respect to F-Rg-MF(2) species, and the computed values are 56.3, 127.8, and 196.0 kJmol for F-Ar-BF(2), F-Kr-BF(2), and F-Xe-BF(2) species, respectively. The corresponding values for F-Ar-AlF(2), F-Kr-AlF(2), and F-Xe-AlF(2) species are also found to be positive. The decomposition of F-Rg-MF(2) species into the MF(3)+Rg (two-body dissociation) channel typically proceeds via a transition state involving F-Rg-M out-of-plane bending mode. The transition state barrier heights are 35.5, 62.7, 89.8, 22.0, 45.6, and 75.3 kJmol for F-Ar-BF(2), F-Kr-BF(2), F-Xe-BF(2), F-Ar-AlF(2), F-Kr-AlF(2), and F-Xe-AlF(2) species, respectively. The calculated geometrical parameters and the energy values suggest that these species are metastable and may be prepared and characterized using low temperature matrix isolation techniques, and are possibly the next new candidates for gas phase or matrix experiments.     

On the origin of Baeyer strain in molecules – an ab initio and DFT analysis

It is shown that destabilization energy of organic molecules containing small rings can be estimated by quasi–homodesmotic reactions involving acyclic “strain–free” counterparts. These destabilization energies E_s can be well reproduced at the HF level employing cc-pVTZ basis set, because the contributions of the electron correlation and ZPV energy practically cancel each other in most cases. A predominating factor leading to a decreased stability of molecules involving small ring fragments is given by the Ω bond bending or Baeyer strain. It leads to a dramatic decrease in the electron–nuclei attraction, which is a hallmark of the angular strain. Similar results are obtained by the DFT–B3LYP method. It is strongly pointed out that Baeyer strain cannot be singled out from the total destabilization energy in a precise quantitative way, since it is interlocked with other types of intramolecular interactions like the nonbonded repulsions, a significant increase in the stability of the CH bonds emanating from the small cyclic structures and by the σ–aromaticity or σ–antiaromaticity in three– and four–membered rings, respectively. Nevertheless, it is fair to say that Baeyer strain is the essential factor in determining decreased stability of small ring compounds and that the diminished electron–nuclear attraction is its characteristic signature at the global level. Dedicated to Professor Karl Jug on the occasion of his 65th birthday.     

Current rectification by asymmetric molecules: an ab initio study

Current rectification effect in an asymmetric molecule HCOO-C6H4-(CH2)n sandwiched between two aluminum electrodes has been studied using an ab initio nonequilibrium Green's function method. The conductance of the system decreases exponentially with the increasing number n of CH2. The phenomenon of current rectification is observed such that a very small current appears at negative bias and a sharp negative differential resistance at a critical positive bias when n>or=2. The rectification effect arises from the asymmetric structure of the molecule and the molecule-electrode couplings. A significant rectification ratio of approximately 38 can be achieved when n=5.     

Glycine interaction with carbon nanotubes: an ab initio study

The interaction of the glycine radical on the side walls of both armchair and zigzag single walled carbon nanotubes is investigated by density functional theory. It is found that the interaction potential of the N-centered glycine radical with the tubes has a minimum of 16.9 (armchair) and 20.2 (zigzag) kcal/mol with respect to the dissociation products. In contrast, the C-centered radical, which is 22.7 kcal/mol lower in energy than the N-centered radical, does not form stable complexes with both types of carbon nanotubes.     

Mutual orientation of two C60 molecules: an ab initio study

The orientational dependence of the interaction between two C(60) molecules is investigated using ab initio calculations. The binding energy, computed within density functional theory in the local density approximation, is substantially smaller than the one derived from the experimental heat of sublimation of fullerite, which calls into question the nature of inter-C(60) bonding. According to our calculations, the experimentally observed orientation with a C(60) presenting a hexagon-hexagon bond to a pentagonal face of the other C(60) is not really favored. Some other configurations are very close in energy and in fact a pentagon facing a pentagon and a hexagon facing a hexagon-hexagon bond are found to be slightly more favorable situations. Our results are compared to previous ones obtained either with previous empirical intermolecular potentials or to existing ab initio studies of crystalline C(60). In addition, the stacking of C(60) in a crystal and in a decahedral (C(60))(7) cluster is discussed.     

Hydrogen bonding and covalent effects in binding of cisplatin to purine bases: ab initio and atoms in molecules studies

Ab initio and density functional calculations are employed to investigate the role of hydrogen bonding in the binding of cisplatin to the purine bases guanine and adenine. Through the use of the theory of atoms in molecules (AIM), it is shown that hydrogen bonds are ubiquitous in such systems, with N-H...N and N-H...Cl interactions present in addition to the expected N-H...O. This in turn means that the known stability of cisplatin-guanine complexes cannot be ascribed solely to hydrogen bonding and allows decomposition of total binding energy into contributions from covalent and hydrogen bonds. To do so, a new method for predicting hydrogen bond energies from bond critical point properties is proposed, employing partial least-squares analysis to remove the family dependence of simple models. Still more hydrogen bond motifs are found in bifunctional complexes of the general type purine-[Pt(NH(3))(2)](2+)-purine, including purine...purine contacts, though again the energetics of these are insufficient to explain the observed trends in stability. Finally, the effect of platination on the pairing of guanine with cytosine is studied in a similar manner, revealing large redistributions of hydrogen bonding but surprisingly small overall changes in pairing energy.     

Interaction of the atoms in molecules of pyridine and its derivatives according to the results of ab initio calculations

Nonempirical quantum-chemical calculations of pyridine and its 2-, 3-, and 4-X-substituted derivatives (X = F, Cl, Br, Me, and Et) by RHF/6-311G(d) and MP2/6-311G(d) methods indicate an alternation of charges on the atoms of the pyridine ring and of the occupancy of their valence p_y-orbitals. This is caused by the polarization of bonds under the action of the charges of the atoms geminal to C(n). Bonding molecular orbitals in these molecules, formed as a result of the p_y-orbitals, occurring in the plane of the pyridine ring, are not an indication (characteristic) of p, π-conjugation between the unshared electron pair of the heteroatom of a substituent X and the π-electron system of the ring. The results of the calculations by these methods did not differ in principle. Dedicated to Academician of the Russian Academy of Sciences M. G. Voronkov in honor of his 85^th birthday. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 11, pp. 1671–1681, November, 2006.     

Insertion of noble gas atoms into cyanoacetylene: an ab initio and matrix isolation study

A computational and experimental matrix isolation study of insertion of noble gas atoms into cyanoacetylene (HCCCN) is presented. Twelve novel noble gas insertion compounds are found to be kinetically stable at the MP2 level of theory, including four molecules with argon. The first group of the computationally studied molecules belongs to noble gas hydrides (HNgCCCN and HNgCCNC), and we found their stability for Ng = Ar, Kr, and Xe. The HNgCCCN compounds with Kr and Xe have similar stability to that of previously reported HKrCN and HXeCN. The HArCCCN molecule seems to have a weaker H-Ar bond than in the previously identified HArF molecule. The HNgCCNC molecules are less stable than the HNgCCCN isomers for all noble gas atoms. The second group of the computational insertion compounds, HCCNgCN and HCCNgNC, are of a different type, and they also are kinetically stable for Ng = Ar, Kr, and Xe. Our photolysis and annealing experiments with low-temperature cyanoacetylene/Ng (Ng = Ar, Kr, and Xe) matrixes evidence the formation of two noble gas hydrides for Ng = Kr and Xe, with the strongest IR absorption bands at 1492.1 and 1624.5 cm(-1), and two additional absorption modes for each species are found. The computational spectra of HKrCCCN and HXeCCCN fit most closely the experimental data, which is the basis for our assignment. The obtained species absorb at quite similar frequencies as the known HKrCN and HXeCN molecules, which is in agreement with the theoretical predictions. No strong candidates for an Ar compound are observed in the IR absorption spectra. As an important side product of this work, the data obtained in long-term decay of KrHKr+ cations suggest a tentative assignment for the CCCN radical.     

硝基烷系列分子的从头计算研究

硝基甲烷作为最简单的硝基类爆炸物,Marynick等曾以各种半经验分子轨道法和从头计算法进行过研究.我们也对其进行过全电子自洽场从头计算,获得有益启示.本文将类似计算用于硝基乙烷、1-和2-硝基丙烷等,发现用其电子结构可阐明各烷基的供电子能力、缩合反应能力、核磁共振谱和热安定性等诸多实验事实.还进行了相应构型和ρ指数下的CNDO/2计算,得到与从头计算平行的结果.     

Structure of N-chloromethyllactams and features of the interaction of atoms in them as a result of ab initio calculations

Quantum-chemical calculations have been carried out by the RHF/6-31G(d) and MP2/6-31+G(d) methods of molecules of N-chloromethylpyrrolidone, N-chloromethylcaprolactam, N-chloromethyl-succinimide, and N-chloromethylphthalimide with full optimization of their geometry, and also N-chloromethylpyrrolidone molecule by the RHF/6-31G(d) method at various angles of rotation of the CH₂Cl group around the C―N bond. It was shown that the lower frequencies of the ³⁵Cl NQR of the first two molecules in comparison with the later are mainly determined by the high populations of the p _σ -orbitals of their Cl atoms. The population of the orbitals of the unshared electron pair of the N atom is practically unchanged on rotating the CH₂Cl group, but the N atom polarizes the C―Cl bond in the indicated molecule. This does not confirm the supposed p,σ*-conjugation in the Cl―C―N grouping. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 10, pp. 1537–1544, October, 2008.     

Accurate energetics of small molecules containing third-row atoms Ga-Kr: a comparison of advanced ab initio and density functional theory

Advanced ab initio [coupled cluster theory through quasiperturbative triple excitations (CCSD(T))] and density functional (B3LYP) computational chemistry approaches were used in combination with the standard and augmented correlation consistent polarized valence basis sets [cc-pVnZ and aug-cc-pVnZ, where n=D(2), T(3), Q(4), and 5] to investigate the energetic and structural properties of small molecules containing third-row (Ga-Kr) atoms. These molecules were taken from the Gaussian-2 (G2) extended test set for third-row atoms. Several different schemes were used to extrapolate the calculated energies to the complete basis set (CBS) limit for CCSD(T) and the Kohn-Sham (KS) limit for B3LYP. Zero point energy and spin orbital corrections were included in the results. Overall, CCSD(T) atomization energies, ionization energies, proton affinities, and electron affinities are in good agreement with experiment, within 1.1 kcal/mol when the CBS limit has been determined using a series of two basis sets of at least triple zeta quality. For B3LYP, the overall mean absolute deviation from experiment for the three properties and the series of molecules is more significant at the KS limit, within 2.3 and 2.6 kcal/mol for the cc-pVnZ and aug-cc-pVnZ basis set series, respectively.     

Simultaneous ab initio calculations of isoelectronic diatomic molecules

Large gaussian basis sets are employed in simultaneous configuration interaction calculations for the ground states of isoelectronic diatomic molecules. The resulting potential energy curves for three members respectively of four different isoelectronic molecule sequences show the applicability of the method. Comparisons with available results of standard configuration interaction calculations for selected molecules are given. Using our method we often get lower upper bounds for the electronic energy, save computer time and treat physically totally different molecules simultaneously.     

Properties of atoms in molecules

Atomic charges calculated by the population analysis method for three types of semi-empirical wave functions have been compared with charges obtained by integrating the corresponding electronic density functions over individual atomic regions. It was found that the two sets of charges compare quite well for CNDO wave functions and for extended-Hückel functions which are in terms of orthogonalized basis orbitals. However only the CNDO charges are reasonably close to those obtained by integrating near-Hartree-Fock electronic density functions.     

Properties of atoms in molecules

The electronic charges and the positions of the centers of these charges have been calculated for the atoms of a number of second- and third-row heteronuclear diatomic molecules. For both the oxygen and the fluorine atoms, the charge associated with one of these atoms can be correlated, within a series of molecules containing that atom, with both the orbital energy of the atom's 1s electrons and also with the difference in electronegativities of the atoms that comprise the molecule. The centers of electronic charge are outside of the internuclear regions, except for the positive atoms in the more ionic molecules and in HF.     

Interaction-induced dipoles of hydrogen molecules colliding with helium atoms: a new ab initio dipole surface for high-temperature applications

We report new ab initio results for the interaction-induced dipole moments Δμ of hydrogen molecules colliding with helium atoms. These results are needed in order to calculate collision-induced absorption spectra at high temperatures; applications include modeling the radiative profiles of very cool white dwarf stars, with temperatures from 3500 K to 9000 K. We have evaluated the dipoles based on finite-field calculations, with coupled cluster methods in MOLPRO 2006 and aug-cc-pV5Z (spdfg) basis sets for both the H and He centers. We have obtained values of Δμ for eight H(2) bond lengths ranging from 0.942 a.u. to 2.801 a.u., for 15 intermolecular separations R ranging from 2.0 a.u. to 10.0 a.u., and for 19 different relative orientations. In general, our values agree well with earlier ab initio results, for the geometrical configurations that are treated in common, but we have determined more points on the collision-induced dipole surface by an order of magnitude. These results make it possible to calculate transition probabilities for molecules in excited vibrational states, overtones, and rotational transitions with ΔJ > 4. We have cast our results in the symmetry-adapted form needed for absorption line shape calculations, by expressing Δμ as a series in the spherical harmonics of the orientation angles of the intermolecular vector and of a unit vector along the H(2) bond axis. The expansion coefficients depend on the H(2) bond length and the intermolecular distance R. For large separations R, we show that the ab initio values of the leading coefficients converge to the predictions from perturbation theory, including both classical multipole polarization and dispersion effects.     

Interaction of molecular SiS with silver atoms in an argon matrix: IR spectrum and ab initio rationalization

Co-condensation of silver atoms and SiS in an argon matrix leads to the formation of Ag(SiS). The IR spectrum can be interpreted in two different ways: Isotopic shifts (²⁸Si/²⁹Si, ²⁸Si/³⁰Si, ³²S/³⁴S) imply a side-on coordination of SiS to silver. On the other hand, the SiS frequency and the isotopic shifts can be assigned to an isolated SiS⁻ molecule. The SiS force constant is reduced from 5.0 mdyn/Å in free SiS to 3.9 mdyn/Å in AgSiS. Ab initio investigations confirm the formation of an ion pair Ag⁺(SiS)⁻, admitting some electron delocalization.     

Nonadiabatic electron wavepacket dynamics of molecules in an intense optical field: an ab initio electronic state study

A theory of quantum electron wavepacket dynamics that nonadiabatically couples with classical nuclear motions in intense optical fields is studied. The formalism is intended to track the laser-driven electron wavepackets in terms of the linear combination of configuration-state functions generated with ab initio molecular orbitals. Beginning with the total quantum Hamiltonian for electrons and nuclei in the vector potential of classical electromagnetic field, we reduce the Hamiltonian into a mixed quantum-classical representation by replacing the quantum nuclear momentum operators with the classical counterparts. This framework gives equations of motion for electron wavepackets in an intense laser field through the time dependent variational principle. On the other hand, a generalization of the Newtonian equations provides a matrix form of forces acting on the nuclei for nonadiabatic dynamics. A mean-field approximation to the force matrix reduces this higher order formalism to the semiclassical Ehrenfest theory in intense optical fields. To bring these theories into a practical quantum chemical package for general molecules, we have implemented the relevant ab initio algorithms in it. Some numerical results in the level of the semiclassical Ehrenfest-type theory with explicit use of the nuclear kinematic (derivative) coupling and the velocity form for the optical interaction are presented.     

An ab initio calculation of K-spectra in molecules HCl and HF

An ab initio calculation of energies and intensities of K-emission and K-absorption spectra in molecules HCl and HF are carried out. An electronic readjustment due to a hole in a molecular core is taken into account. A vibrational structure of K-emission and K-absorption spectra is also calculated. The calculation shows that it is possible to detect a vibrational structure of valence bonding levels in X-ray emission spectra. A good agreement with experiment is obtained.